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- PDB-3aqe: Crystal structure of the extracellular domain of human RAMP2 -

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Basic information

Entry
Database: PDB / ID: 3aqe
TitleCrystal structure of the extracellular domain of human RAMP2
ComponentsReceptor activity-modifying protein 2
KeywordsTRANSPORT PROTEIN / Transmembrane / GPCR / Adrenomedullin / TRAFFICKING / CLR / CGRP / Endoplasmic Reticulum / DISEASE / Neovascularization / Helix bundle / Calcitonin Receptor-Like Receptor (CRLR) / Endoplasmic Reticulum (ER) / Cell membrane
Function / homology
Function and homology information


basement membrane assembly / adrenomedullin binding / adrenomedullin receptor activity / adrenomedullin receptor complex / vascular associated smooth muscle cell development / adrenomedullin receptor signaling pathway / Calcitonin-like ligand receptors / positive regulation of vasculogenesis / bicellular tight junction assembly / regulation of G protein-coupled receptor signaling pathway ...basement membrane assembly / adrenomedullin binding / adrenomedullin receptor activity / adrenomedullin receptor complex / vascular associated smooth muscle cell development / adrenomedullin receptor signaling pathway / Calcitonin-like ligand receptors / positive regulation of vasculogenesis / bicellular tight junction assembly / regulation of G protein-coupled receptor signaling pathway / adherens junction assembly / negative regulation of vascular permeability / sprouting angiogenesis / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / negative regulation of endothelial cell apoptotic process / coreceptor activity / clathrin-coated pit / cellular response to hormone stimulus / protein localization to plasma membrane / intracellular protein transport / adenylate cyclase-activating G protein-coupled receptor signaling pathway / receptor internalization / regulation of blood pressure / positive regulation of angiogenesis / calcium ion transport / protein transport / heart development / G alpha (s) signalling events / angiogenesis / lysosome / receptor complex / G protein-coupled receptor signaling pathway / positive regulation of gene expression / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Receptor activity modifying family / Receptor activity modifying protein / RAMP domain superfamily / Receptor activity modifying family / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Receptor activity-modifying protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKusano, S. / Kukimoto-Niino, M. / Shirouzu, M. / Shindo, T. / Yokoyama, S.
CitationJournal: Protein Sci. / Year: 2012
Title: Structural basis for extracellular interactions between calcitonin receptor-like receptor and receptor activity-modifying protein 2 for adrenomedullin-specific binding
Authors: Kusano, S. / Kukimoto-Niino, M. / Hino, N. / Ohsawa, N. / Okuda, K. / Sakamoto, K. / Shirouzu, M. / Shindo, T. / Yokoyama, S.
History
DepositionOct 29, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor activity-modifying protein 2
B: Receptor activity-modifying protein 2
C: Receptor activity-modifying protein 2
D: Receptor activity-modifying protein 2
E: Receptor activity-modifying protein 2
F: Receptor activity-modifying protein 2


Theoretical massNumber of molelcules
Total (without water)63,4896
Polymers63,4896
Non-polymers00
Water5,080282
1
A: Receptor activity-modifying protein 2


Theoretical massNumber of molelcules
Total (without water)10,5811
Polymers10,5811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor activity-modifying protein 2


Theoretical massNumber of molelcules
Total (without water)10,5811
Polymers10,5811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Receptor activity-modifying protein 2


Theoretical massNumber of molelcules
Total (without water)10,5811
Polymers10,5811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Receptor activity-modifying protein 2


Theoretical massNumber of molelcules
Total (without water)10,5811
Polymers10,5811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Receptor activity-modifying protein 2


Theoretical massNumber of molelcules
Total (without water)10,5811
Polymers10,5811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Receptor activity-modifying protein 2


Theoretical massNumber of molelcules
Total (without water)10,5811
Polymers10,5811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Receptor activity-modifying protein 2
B: Receptor activity-modifying protein 2
C: Receptor activity-modifying protein 2


Theoretical massNumber of molelcules
Total (without water)31,7443
Polymers31,7443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-27 kcal/mol
Surface area11580 Å2
MethodPISA
8
D: Receptor activity-modifying protein 2
E: Receptor activity-modifying protein 2
F: Receptor activity-modifying protein 2


Theoretical massNumber of molelcules
Total (without water)31,7443
Polymers31,7443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-27 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.571, 89.729, 91.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Receptor activity-modifying protein 2 / Calcitonin-receptor-like receptor activity-modifying protein 2 / CRLR activity-modifying protein 2


Mass: 10581.471 Da / Num. of mol.: 6 / Fragment: extracellular Domain, UNP residues 56-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAMP2 / Plasmid: PX070809-03 / Production host: Escherichia coli cell-free system / References: UniProt: O60895
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M Sodium-HEPES, 25% (v/v) PEG 400, 0.2M Calcium chloride di-hydrate, 0.15% Agarose , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9788, 0.9792, 0.9640
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 6, 2008
RadiationMonochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97921
30.9641
ReflectionResolution: 2→50 Å / Num. obs: 33866 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.62 % / Rsym value: 0.084 / Net I/σ(I): 19.3
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 7.7 / Rsym value: 0.24 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX1.7.2_869refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→36.408 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7331 / SU ML: 0.37 / Isotropic thermal model: RESTRAINED / σ(F): 1.33 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2762 1696 5.07 %
Rwork0.2304 --
obs0.2328 33465 97.92 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.941 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 124.91 Å2 / Biso mean: 28.0343 Å2 / Biso min: 7.88 Å2
Baniso -1Baniso -2Baniso -3
1--7.9188 Å20 Å2-0 Å2
2--10.5264 Å2-0 Å2
3----2.6076 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→36.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 0 282 4091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033959
X-RAY DIFFRACTIONf_angle_d0.9425375
X-RAY DIFFRACTIONf_dihedral_angle_d15.9241397
X-RAY DIFFRACTIONf_chiral_restr0.071537
X-RAY DIFFRACTIONf_plane_restr0.004705
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9967-2.05540.26231330.23442588272198
2.0554-2.12180.31761260.25326762802100
2.1218-2.19760.32531430.26582632277598
2.1976-2.28560.39871410.35222284242586
2.2856-2.38960.34341380.25522574271296
2.3896-2.51550.29731330.230326582791100
2.5155-2.67310.3011500.234226852835100
2.6731-2.87940.26981380.233527122850100
2.8794-3.1690.28321360.234527062842100
3.169-3.62720.23941490.21022699284899
3.6272-4.56850.23351340.18612759289399
4.5685-36.41420.24541750.2242796297198
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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